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VirologyCharite / convert-spread3

A horrible shell script hack to convert SpreadD3 output files for Christian
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How to execute the convert-spread3.sh? #1

Closed virologist closed 4 years ago

virologist commented 4 years ago

Hi, Terry

Recently, I am trying to use SpreaD3 to interpret the phylogeographic diffusion of flu. I meet as same as the error described in https://github.com/phylogeography/SpreaD3/issues/32. I struggled here for many hours. Then I found your solutions. Very nice. It's relief me. However, I don't know how to use this .sh. Could you please give me some clues? I try PowerShell on my win 10 and WSL. Neither of them works well. I put the snapshots of the errors I take. image image image Thanks a lot!

Best regards, Yan

terrycojones commented 4 years ago

Hi Yan. I don't use windows, so this may not work. Using WSL is the best option. Try this:

$ mkdir /tmp
$ apt-get install awk sed

You may need to put sudo before that final command, but I don't know if that exists or is needed on windows. Then try re-running.

virologist commented 4 years ago

Thank you very much, Terry. I made it.

$ mkdir tmp
$ sudo apt-get install awk sed
$ bash convert-spread3.sh
terrycojones commented 4 years ago

Great - good on you for digging into this and getting it all the way fixed on your system! That's really nice to hear and you are in a minority! :-) Best of luck with your work.

virologist commented 4 years ago

Thank you very much! Without your code and tutorial, I can’t move forward a single step.

Best regard

From: Terry Jonesmailto:notifications@github.com Sent: Thursday, June 4, 2020 10:58 PM To: VirologyCharite/convert-spread3mailto:convert-spread3@noreply.github.com Cc: Biopigmailto:virolog@outlook.com; State changemailto:state_change@noreply.github.com Subject: Re: [VirologyCharite/convert-spread3] How to execute the convert-spread3.sh? (#1)

Great - good on you for digging into this and getting it all the way fixed on your system! That's really nice to hear and you are in a minority! :-) Best of luck with your work.

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